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  <h1>Source code for complete_install</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">errno</span>
<span class="kn">import</span> <span class="nn">argparse</span>
<span class="kn">from</span> <span class="nn">subprocess</span> <span class="kn">import</span> <span class="n">call</span><span class="p">,</span> <span class="n">PIPE</span><span class="p">,</span> <span class="n">Popen</span>

<span class="n">HOME_DIR</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;HOME&#39;</span><span class="p">)</span>


<div class="viewcode-block" id="install_pysimm"><a class="viewcode-back" href="../complete_install.html#complete_install.install_pysimm">[docs]</a><span class="k">def</span> <span class="nf">install_pysimm</span><span class="p">(</span><span class="n">prefix</span><span class="p">):</span>
    <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span>
    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="s1">&#39;pysimm&#39;</span><span class="p">):</span>
        <span class="k">print</span><span class="p">(</span><span class="s1">&#39;pysimm directory already exists...assuming it is the pysimm repository and continuing...&#39;</span><span class="p">)</span>
    <span class="k">else</span><span class="p">:</span>
        <span class="n">call</span><span class="p">(</span><span class="s1">&#39;git clone https://github.com/polysimtools/pysimm&#39;</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="s1">&#39;pysimm/complete_install.py&#39;</span><span class="p">):</span>
        <span class="k">print</span><span class="p">(</span><span class="s1">&#39;assumption about pysimm repository existing was wrong; exiting...&#39;</span><span class="p">)</span>
        <span class="nb">exit</span><span class="p">()</span>
    <span class="n">call</span><span class="p">(</span><span class="s2">&quot;echo export PYTHONPATH=&#39;$PYTHONPATH&#39;:{} &gt;&gt; {}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="s1">&#39;pysimm&#39;</span><span class="p">),</span>
                                                                <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">,</span> <span class="s1">&#39;.bashrc&#39;</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s2">&quot;echo export PATH=&#39;$PATH&#39;:{} &gt;&gt; {}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="s1">&#39;pysimm&#39;</span><span class="p">,</span> <span class="s1">&#39;bin&#39;</span><span class="p">),</span>
                                                    <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">,</span> <span class="s1">&#39;.bashrc&#39;</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span></div>


<div class="viewcode-block" id="apt_update"><a class="viewcode-back" href="../complete_install.html#complete_install.apt_update">[docs]</a><span class="k">def</span> <span class="nf">apt_update</span><span class="p">():</span>
    <span class="n">call</span><span class="p">(</span><span class="s1">&#39;apt-get update&#39;</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span></div>


<div class="viewcode-block" id="apt_install"><a class="viewcode-back" href="../complete_install.html#complete_install.apt_install">[docs]</a><span class="k">def</span> <span class="nf">apt_install</span><span class="p">(</span><span class="o">*</span><span class="n">packages</span><span class="p">):</span>
    <span class="n">call</span><span class="p">(</span><span class="s1">&#39;apt-get -y install {}&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">packages</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span></div>


<div class="viewcode-block" id="install_lammps"><a class="viewcode-back" href="../complete_install.html#complete_install.install_lammps">[docs]</a><span class="k">def</span> <span class="nf">install_lammps</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="o">*</span><span class="n">packages</span><span class="p">):</span>
    <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s1">&#39;git clone -b unstable https://github.com/lammps/lammps.git lammps&#39;</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span><span class="s1">&#39;lammps&#39;</span><span class="p">,</span><span class="s1">&#39;src&#39;</span><span class="p">))</span>
    <span class="k">for</span> <span class="n">package</span> <span class="ow">in</span> <span class="n">packages</span><span class="p">:</span>
        <span class="n">call</span><span class="p">(</span><span class="s1">&#39;make yes-{}&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">package</span><span class="p">),</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s1">&#39;make mpi&#39;</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s2">&quot;echo export PATH=&#39;$PATH&#39;:{} &gt;&gt; {}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="s1">&#39;lammps&#39;</span><span class="p">,</span> <span class="s1">&#39;src&#39;</span><span class="p">),</span>
                                                    <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">,</span><span class="s1">&#39;.bashrc&#39;</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s2">&quot;echo export LAMMPS_EXEC={} &gt;&gt; {}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="s1">&#39;lammps&#39;</span><span class="p">,</span> <span class="s1">&#39;src&#39;</span><span class="p">,</span> <span class="s1">&#39;lmp_mpi&#39;</span><span class="p">),</span>
                                                   <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">,</span><span class="s1">&#39;.bashrc&#39;</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span></div>
         
<div class="viewcode-block" id="install_ambertools"><a class="viewcode-back" href="../complete_install.html#complete_install.install_ambertools">[docs]</a><span class="k">def</span> <span class="nf">install_ambertools</span><span class="p">(</span><span class="n">dir_</span><span class="p">):</span>
    <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">dir_</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s2">&quot;echo export AMBERHOME={} &gt;&gt; {}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">dir_</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">,</span><span class="s1">&#39;.bashrc&#39;</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;AMBERHOME&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">dir_</span>
    <span class="n">call</span><span class="p">(</span><span class="s1">&#39;./configure gnu&#39;</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s1">&#39;make install&#39;</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    <span class="n">call</span><span class="p">(</span><span class="s2">&quot;echo export ANTECHAMBER_EXEC={} &gt;&gt; {}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">dir_</span><span class="p">,</span> <span class="s1">&#39;bin&#39;</span><span class="p">,</span> <span class="s1">&#39;antechamber&#39;</span><span class="p">),</span>
                                                   <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">,</span><span class="s1">&#39;.bashrc&#39;</span><span class="p">)),</span>
         <span class="n">shell</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span></div>
         
<div class="viewcode-block" id="install_openbabel"><a class="viewcode-back" href="../complete_install.html#complete_install.install_openbabel">[docs]</a><span class="k">def</span> <span class="nf">install_openbabel</span><span class="p">():</span>
    <span class="n">apt_install</span><span class="p">(</span><span class="s1">&#39;libopenbabel4&#39;</span><span class="p">,</span> <span class="s1">&#39;libopenbabel-dev&#39;</span><span class="p">,</span> <span class="s1">&#39;openbabel&#39;</span><span class="p">,</span> <span class="s1">&#39;python-openbabel&#39;</span><span class="p">)</span></div>


<div class="viewcode-block" id="parse_args"><a class="viewcode-back" href="../complete_install.html#complete_install.parse_args">[docs]</a><span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
    <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">()</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--apt-update&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;apt_update&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--apt-install&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;apt_install&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--pysimm&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;pysimm_prefix&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="n">HOME_DIR</span><span class="p">)</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--lammps&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;lammps_prefix&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--lammps-packages&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;lammps_packages&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span>
                        <span class="n">default</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;molecule&#39;</span><span class="p">,</span> <span class="s1">&#39;class2&#39;</span><span class="p">,</span> <span class="s1">&#39;kspace&#39;</span><span class="p">,</span> <span class="s1">&#39;user-misc&#39;</span><span class="p">,</span> <span class="s1">&#39;misc&#39;</span><span class="p">,</span> <span class="s1">&#39;qeq&#39;</span><span class="p">,</span> <span class="s1">&#39;manybody&#39;</span><span class="p">])</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--amber-tools&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;ambertools_dir&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span>
    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--openbabel&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;openbabel&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
    <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>


<div class="viewcode-block" id="mkdir_p"><a class="viewcode-back" href="../complete_install.html#complete_install.mkdir_p">[docs]</a><span class="k">def</span> <span class="nf">mkdir_p</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
    <span class="k">try</span><span class="p">:</span>
        <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
    <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">exc</span><span class="o">.</span><span class="n">errno</span> <span class="o">==</span> <span class="n">errno</span><span class="o">.</span><span class="n">EEXIST</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
            <span class="k">pass</span>
        <span class="k">else</span><span class="p">:</span>
            <span class="k">raise</span></div>


<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>

    <span class="n">args</span> <span class="o">=</span> <span class="n">parse_args</span><span class="p">()</span>

    <span class="k">if</span> <span class="nb">bool</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">apt_update</span><span class="p">):</span>
        <span class="n">apt_update</span><span class="p">()</span>

    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">pysimm_prefix</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">apt_install</span><span class="p">:</span>
            <span class="n">apt_install</span><span class="p">(</span><span class="s1">&#39;git&#39;</span><span class="p">,</span> <span class="s1">&#39;python-numpy&#39;</span><span class="p">,</span> <span class="s1">&#39;python-matplotlib&#39;</span><span class="p">)</span>
        <span class="n">mkdir_p</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">pysimm_prefix</span><span class="p">)</span>
        <span class="n">install_pysimm</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">pysimm_prefix</span><span class="p">)</span>

    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">lammps_prefix</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">apt_install</span><span class="p">:</span>
            <span class="n">apt_install</span><span class="p">(</span><span class="s1">&#39;make git g++&#39;</span><span class="p">,</span> <span class="s1">&#39;libopenmpi-dev&#39;</span><span class="p">,</span> <span class="s1">&#39;openmpi-bin&#39;</span><span class="p">)</span>
        <span class="n">mkdir_p</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">lammps_prefix</span><span class="p">)</span>
        <span class="n">install_lammps</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">lammps_prefix</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="o">.</span><span class="n">lammps_packages</span><span class="p">)</span>
        
    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">ambertools_dir</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">apt_install</span><span class="p">:</span>
            <span class="n">apt_install</span><span class="p">(</span><span class="s1">&#39;make&#39;</span><span class="p">,</span> <span class="s1">&#39;csh&#39;</span><span class="p">,</span> <span class="s1">&#39;gfortran&#39;</span><span class="p">,</span> <span class="s1">&#39;libopenmpi-dev&#39;</span><span class="p">,</span> <span class="s1">&#39;openmpi-bin&#39;</span><span class="p">,</span> <span class="s1">&#39;xorg-dev&#39;</span><span class="p">,</span> <span class="s1">&#39;xserver-xorg&#39;</span><span class="p">)</span>
        <span class="n">install_ambertools</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">ambertools_dir</span><span class="p">)</span>
        
    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">openbabel</span><span class="p">:</span>
        <span class="n">install_openbabel</span><span class="p">()</span>
        
    <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">HOME_DIR</span><span class="p">)</span>

</pre></div>

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